Genome annotation with Braker3
1.0

Workflow Type: Galaxy

This workflow uses Braker3 to annotate a genome.

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Braker3, available in the GTN

Features

Thanks to...

Workflow Author(s): Romane Libouban

Tutorial Author(s): Romane LIBOUBAN, Anthony Bretaudeau

Tutorial Contributor(s): Deepti Varshney, Saskia Hiltemann, Bérénice Batut

Grants(s): EuroScienceGateway

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Alignments from RNA-seq Alignments from RNA-seq Alignments from RNA-seq
  • File
BUSCO lineage BUSCO lineage BUSCO lineage
  • string
Genome sequence masked Genome sequence masked Genome sequence
  • File
Protein sequences Protein sequences Protein sequences
  • File

Steps

ID Name Description
4 Fasta Statistics Fasta Statistics on the genome toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0
5 BUSCO on the genome sequences Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0
6 Braker3 Genome annotation with Braker3 toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/3.0.8+galaxy0
7 GFFRead Converts GFF files to other formats, such as FASTA toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0
8 JBrowse toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1
9 BUSCO on the predicted protein sequences Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0

Outputs

ID Name Description Type
fasta stats genome fasta stats genome n/a
  • File
busco table genome busco table genome n/a
  • File
busco sum genome busco sum genome n/a
  • File
busco image genome busco image genome n/a
  • File
busco missing genome busco missing genome n/a
  • File
busco gff genome busco gff genome n/a
  • File
braker gff braker gff n/a
  • File
predicted proteins predicted proteins n/a
  • File
jbrowse jbrowse n/a
  • File
busco image predicted proteins busco image predicted proteins n/a
  • File
busco gff predicted proteins busco gff predicted proteins n/a
  • File
busco sum predicted proteins busco sum predicted proteins n/a
  • File
busco missing predicted proteins busco missing predicted proteins n/a
  • File
busco table predicted proteins busco table predicted proteins n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:56 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:56

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